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2. Data‐driven identification of environmental variables influencing phenotypic plasticity to facilitate breeding for future climates.

Author

Kusmec, Aaron, Yeh, Cheng‐Ting 'Eddy', Bohn, Martin O., Campbell, Darwin A., Ciampitti, Ignacio A., Ertl, David S., Flint‐Garcia, Sherry A., Gore, Michael A., Hirsch, Candice N., Kaeppler, Shawn M., Knoll, Joseph E., Kolkman, Judith M., Lauter, Nick, Lawrence‐Dill, Carolyn J., Lee, Elizabeth C., de Leon, Natalia, Liu, Sanzhen, Lorence, Argelia, Schnable, James C., and Sekhon, Rajandeep S.

Subjects
*PLANT breeding, *PHENOTYPIC plasticity, *GENETIC algorithms, *GRAIN yields, *AGRICULTURAL climatology
Abstract

Summary: Phenotypic plasticity describes a genotype's ability to produce different phenotypes in response to different environments. Breeding crops that exhibit appropriate levels of plasticity for future climates will be crucial to meeting global demand, but knowledge of the critical environmental factors is limited to a handful of well‐studied major crops.Using 727 maize (Zea mays L.) hybrids phenotyped for grain yield in 45 environments, we investigated the ability of a genetic algorithm and two other methods to identify environmental determinants of grain yield from a large set of candidate environmental variables constructed using minimal assumptions.The genetic algorithm identified pre‐ and postanthesis maximum temperature, mid‐season solar radiation, and whole season net evapotranspiration as the four most important variables from a candidate set of 9150. Importantly, these four variables are supported by previous literature. After calculating reaction norms for each environmental variable, candidate genes were identified and gene annotations investigated to demonstrate how this method can generate insights into phenotypic plasticity.The genetic algorithm successfully identified known environmental determinants of hybrid maize grain yield. This demonstrates that the methodology could be applied to other less well‐studied phenotypes and crops to improve understanding of phenotypic plasticity and facilitate breeding crops for future climates. [ABSTRACT FROM AUTHOR]

Published
2024
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3. Detailed analysis of a contiguous 22-Mb region of the maize genome.

Author

Wei, Fusheng, Stein, Joshua C, Liang, Chengzhi, Zhang, Jianwei, Fulton, Robert S, Baucom, Regina S, De Paoli, Emanuele, Zhou, Shiguo, Yang, Lixing, Han, Yujun, Pasternak, Shiran, Narechania, Apurva, Zhang, Lifang, Yeh, Cheng-Ting, Ying, Kai, Nagel, Dawn H, Collura, Kristi, Kudrna, David, Currie, Jennifer, Lin, Jinke, Kim, Hyeran, Angelova, Angelina, Scara, Gabriel, Wissotski, Marina, Golser, Wolfgang, Courtney, Laura, Kruchowski, Scott, Graves, Tina A, Rock, Susan M, Adams, Stephanie, Fulton, Lucinda A, Fronick, Catrina, Courtney, William, Kramer, Melissa, Spiegel, Lori, Nascimento, Lydia, Kalyanaraman, Ananth, Chaparro, Cristian, Deragon, Jean-Marc, Miguel, Phillip San, Jiang, Ning, Wessler, Susan R, Green, Pamela J, Yu, Yeisoo, Schwartz, David C, Meyers, Blake C, Bennetzen, Jeffrey L, Martienssen, Robert A, McCombie, W Richard, Aluru, Srinivas, Clifton, Sandra W, Schnable, Patrick S, Ware, Doreen, Wilson, Richard K, and Wing, Rod A

Subjects
Chromosomes, Plant, Sorghum, Zea mays, DNA Transposable Elements, RNA, Plant, Physical Chromosome Mapping, Evolution, Molecular, Gene Rearrangement, Gene Duplication, Base Sequence, Base Pairing, Sequence Homology, Nucleic Acid, Synteny, Mutation, Genes, Plant, Genome, Plant, Open Reading Frames, Molecular Sequence Data, Genetic Loci, Oryza, Chromosomes, Plant, Evolution, Molecular, Genes, Genome, RNA, Sequence Homology, Nucleic Acid, Genetics, Developmental Biology
Abstract

Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of transposable elements (TEs) that are mostly nested within each other, of which most families are low-copy. We identified 544 gene models using multiple levels of evidence, as well as five miRNA genes. Gene fragments, many captured by TEs, are prevalent within this region. Elimination of gene redundancy from a tetraploid maize ancestor that originated a few million years ago is responsible in this region for most disruptions of synteny with sorghum and rice. Consistent with other sub-genomic analyses in maize, small RNA mapping showed that many small RNAs match TEs and that most TEs match small RNAs. These results, performed on approximately 1% of the maize genome, demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets. Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses.

Published
2009

5. Maize genomes to fields (G2F): 2014–2017 field seasons: genotype, phenotype, climatic, soil, and inbred ear image datasets

Author

McFarland, Bridget A., AlKhalifah, Naser, Bohn, Martin, Bubert, Jessica, Buckler, Edward S., Ciampitti, Ignacio, Edwards, Jode, Ertl, David, Gage, Joseph L., Falcon, Celeste M., Flint-Garcia, Sherry, Gore, Michael A., Graham, Christopher, Hirsch, Candice N., Holland, James B., Hood, Elizabeth, Hooker, David, Jarquin, Diego, Kaeppler, Shawn M., Knoll, Joseph, Kruger, Greg, Lauter, Nick, Lee, Elizabeth C., Lima, Dayane C., Lorenz, Aaron, Lynch, Jonathan P., McKay, John, Miller, Nathan D., Moose, Stephen P., Murray, Seth C., Nelson, Rebecca, Poudyal, Christina, Rocheford, Torbert, Rodriguez, Oscar, Romay, Maria Cinta, Schnable, James C., Schnable, Patrick S., Scully, Brian, Sekhon, Rajandeep, Silverstein, Kevin, Singh, Maninder, Smith, Margaret, Spalding, Edgar P., Springer, Nathan, Thelen, Kurt, Thomison, Peter, Tuinstra, Mitchell, Wallace, Jason, Walls, Ramona, Wills, David, Wisser, Randall J., Xu, Wenwei, Yeh, Cheng-Ting, and de Leon, Natalia

Published
2020
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11. Maize Genomes to Fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets

Author

AlKhalifah, Naser, Campbell, Darwin A., Falcon, Celeste M., Gardiner, Jack M., Miller, Nathan D., Romay, Maria Cinta, Walls, Ramona, Walton, Renee, Yeh, Cheng-Ting, Bohn, Martin, Bubert, Jessica, Buckler, Edward S., Ciampitti, Ignacio, Flint-Garcia, Sherry, Gore, Michael A., Graham, Christopher, Hirsch, Candice, Holland, James B., Hooker, David, Kaeppler, Shawn, Knoll, Joseph, Lauter, Nick, Lee, Elizabeth C., Lorenz, Aaron, Lynch, Jonathan P., Moose, Stephen P., Murray, Seth C., Nelson, Rebecca, Rocheford, Torbert, Rodriguez, Oscar, Schnable, James C., Scully, Brian, Smith, Margaret, Springer, Nathan, Thomison, Peter, Tuinstra, Mitchell, Wisser, Randall J., Xu, Wenwei, Ertl, David, Schnable, Patrick S., De Leon, Natalia, Spalding, Edgar P., Edwards, Jode, and Lawrence-Dill, Carolyn J.

Published
2018
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14. The B73 Maize Genome: Complexity, Diversity, and Dynamics

Author

Schnable, Patrick S., Ware, Doreen, Fulton, Robert S., Stein, Joshua C., Wei, Fusheng, Pasternak, Shiran, Liang, Chengzhi, Zhang, Jianwei, Fulton, Lucinda, Graves, Tina A., Minx, Patrick, Reily, Amy Denise, Courtney, Laura, Kruchowski, Scott S., Tomlinson, Chad, Strong, Cindy, Delehaunty, Kim, Fronick, Catrina, Courtney, Bill, Rock, Susan M., Belter, Eddie, Du, Feiyu, Kim, Kyung, Abbott, Rachel M., Cotton, Marc, Levy, Andy, Marchetto, Pamela, Ochoa, Kerri, Jackson, Stephanie M., Gillam, Barbara, Chen, Weizu, Yan, Le, Higginbotham, Jamey, Cardenas, Marco, Waligorski, Jason, Applebaum, Elizabeth, Phelps, Lindsey, Falcone, Jason, Kanchi, Krishna, Thane, Thynn, Scimone, Adam, Thane, Nay, Henke, Jessica, Wang, Tom, Ruppert, Jessica, Shah, Neha, Rotter, Kelsi, Hodges, Jennifer, Ingenthron, Elizabeth, Cordes, Matt, Kohlberg, Sara, Sgro, Jennifer, Delgado, Brandon, Mead, Kelly, Chinwalla, Asif, Leonard, Shawn, Crouse, Kevin, Collura, Kristi, Kudrna, Dave, Currie, Jennifer, He, Ruifeng, Angelova, Angelina, Rajasekar, Shanmugam, Mueller, Teri, Lomeli, Rene, Scara, Gabriel, Ko, Ara, Delaney, Krista, Wissotski, Marina, Lopez, Georgina, Campos, David, Braidotti, Michele, Ashley, Elizabeth, Golser, Wolfgang, Kim, HyeRan, Lee, Seunghee, Lin, Jinke, Dujmic, Zeljko, Kim, Woojin, Talag, Jayson, Zuccolo, Andrea, Fan, Chuanzhu, Sebastian, Aswathy, Kramer, Melissa, Spiegel, Lori, Nascimento, Lidia, Zutavern, Theresa, Miller, Beth, Ambroise, Claude, Muller, Stephanie, Spooner, Will, Narechania, Apurva, Ren, Liya, Wei, Sharon, Kumari, Sunita, Faga, Ben, Levy, Michael J., McMahan, Linda, Van Buren, Peter, Vaughn, Matthew W., Ying, Kai, Yeh, Cheng-Ting, Emrich, Scott J., Jia, Yi, Kalyanaraman, Ananth, Hsia, An-Ping, Barbazuk, W. Brad, Baucom, Regina S., Brutnell, Thomas P., Carpita, Nicholas C., Chaparro, Cristian, Chia, Jer-Ming, Deragon, Jean-Marc, Estill, James C., Fu, Yan, Jeddeloh, Jeffrey A., Han, Yujun, Lee, Hyeran, Li, Pinghua, Lisch, Damon R., Liu, Sanzhen, Liu, Zhijie, Nagel, Dawn Holligan, McCann, Maureen C., SanMiguel, Phillip, Myers, Alan M., Nettleton, Dan, Nguyen, John, Penning, Bryan W., Ponnala, Lalit, Schneider, Kevin L., Schwartz, David C., Sharma, Anupma, Soderlund, Carol, Springer, Nathan M., Sun, Qi, Wang, Hao, Waterman, Michael, Westerman, Richard, Wolfgruber, Thomas K., Yang, Lixing, Yu, Yeisoo, Zhang, Lifang, Zhou, Shiguo, Zhu, Qihui, Bennetzen, Jeffrey L., Dawe, R. Kelly, Jiang, Jiming, Jiang, Ning, Presting, Gernot G., Wessler, Susan R., Aluru, Srinivas, Martienssen, Robert A., Clifton, Sandra W., McCombie, W. Richard, Wing, Rod A., and Wilson, Richard K.

Published
2009
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18. Trajectories of Homoeolog-Specific Expression in Allotetraploid Tragopogon castellanus Populations of Independent Origins

Author

University of Florida, College of Liberal Arts and Sciences, University of Florida, Genetics Institute, University of Florida, National Science Foundation (US), Boatwright, J. Lucas, Yeh, Cheng-Ting, Hu, Heng-Cheng, Susanna de la Serna, Alfonso, Soltis, Douglas E., Soltis, Pamela S., Schnable, Patrick S., Barbazuk, William B., University of Florida, College of Liberal Arts and Sciences, University of Florida, Genetics Institute, University of Florida, National Science Foundation (US), Boatwright, J. Lucas, Yeh, Cheng-Ting, Hu, Heng-Cheng, Susanna de la Serna, Alfonso, Soltis, Douglas E., Soltis, Pamela S., Schnable, Patrick S., and Barbazuk, William B.

Abstract

Polyploidization can have a significant ecological and evolutionary impact by providing substantially more genetic material that may result in novel phenotypes upon which selection may act. While the effects of polyploidization are broadly reviewed across the plant tree of life, the reproducibility of these effects within naturally occurring, independently formed polyploids is poorly characterized. The flowering plant genus Tragopogon (Asteraceae) offers a rare glimpse into the intricacies of repeated allopolyploid formation with both nascent (< 90 years old) and more ancient (mesopolyploids) formations. Neo- and mesopolyploids in Tragopogon have formed repeatedly and have extant diploid progenitors that facilitate the comparison of genome evolution after polyploidization across a broad span of evolutionary time. Here, we examine four independently formed lineages of the mesopolyploid Tragopogon castellanus for homoeolog expression changes and fractionation after polyploidization. We show that expression changes are remarkably similar among these independently formed polyploid populations with large convergence among expressed loci, moderate convergence among loci lost, and stochastic silencing. We further compare and contrast these results for T. castellanus with two nascent Tragopogon allopolyploids. While homoeolog expression bias was balanced in both nascent polyploids and T. castellanus, the degree of additive expression was significantly different, with the mesopolyploid populations demonstrating more non-additive expression. We suggest that gene dosage and expression noise minimization may play a prominent role in regulating gene expression patterns immediately after allopolyploidization as well as deeper into time, and these patterns are conserved across independent polyploid lineages.

Published
2021

25. Repeat subtraction-mediated sequence capture from a complex genome

Author

Fu, Yan, Springer, Nathan M., Gerhardt, Daniel J., Ying, Kai, Yeh, Cheng-Ting, Wu, Wei, Swanson-Wagner, Ruth, DʼAscenzo, Mark, Millard, Tracy, Freeberg, Lindsay, Aoyama, Natsuyo, Kitzman, Jacob, Burgess, Daniel, Richmond, Todd, Albert, Thomas J., Barbazuk, Brad W., Jeddeloh, Jeffrey A., and Schnable, Patrick S.

Published
2010
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26. Co‐expression analysis aids in the identification of genes in the cuticular wax pathway in maize

Author

Zheng, Jun, primary, He, Cheng, additional, Qin, Yang, additional, Lin, Guifang, additional, Park, Woojun D., additional, Sun, Minghao, additional, Li, Jian, additional, Lu, Xiaoduo, additional, Zhang, Chunyi, additional, Yeh, Cheng‐Ting, additional, Gunasekara, Chathura J., additional, Zeng, Erliang, additional, Wei, Hairong, additional, Schnable, Patrick S., additional, Wang, Guoying, additional, and Liu, Sanzhen, additional

Published
2018
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27. Empirical Comparisons of Different Statistical Models To Identify and Validate Kernel Row Number-Associated Variants from Structured Multi-parent Mapping Populations of Maize

Author

Yang, Jinliang, primary, Yeh, Cheng-Ting “Eddy”, additional, Ramamurthy, Raghuprakash Kastoori, additional, Qi, Xinshuai, additional, Fernando, Rohan L, additional, Dekkers, Jack C M, additional, Garrick, Dorian J, additional, Nettleton, Dan, additional, and Schnable, Patrick S, additional

Published
2018
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29. Phenotypic Data from Inbred Parents Can Improve Genomic Prediction in Pearl Millet Hybrids

Author

Liang, Zhikai, primary, Gupta, Shashi K, additional, Yeh, Cheng-Ting, additional, Zhang, Yang, additional, Ngu, Daniel W, additional, Kumar, Ramesh, additional, Patil, Hemant T, additional, Mungra, Kanulal D, additional, Yadav, Dev Vart, additional, Rathore, Abhishek, additional, Srivastava, Rakesh K, additional, Gupta, Rajeev, additional, Yang, Jinliang, additional, Varshney, Rajeev K, additional, Schnable, Patrick S, additional, and Schnable, James C, additional

Published
2018
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34. Co‐expression analysis aids in the identification of genes in the cuticular wax pathway in maize.

Author

Zheng, Jun, He, Cheng, Qin, Yang, Lin, Guifang, Park, Woojun D., Sun, Minghao, Li, Jian, Lu, Xiaoduo, Zhang, Chunyi, Yeh, Cheng‐Ting, Gunasekara, Chathura J., Zeng, Erliang, Wei, Hairong, Schnable, Patrick S., Wang, Guoying, and Liu, Sanzhen

Subjects
CORN, WAXES, ENVIRONMENTAL engineering, TRANSCRIPTOMES, TRANSCRIPTION factors, GENE expression
Abstract

Summary: Epicuticular waxes provide a hydrophobic barrier that protects land plants from environmental stresses. To elucidate the molecular functions of maize glossy mutants that reduce the accumulation of epicuticular waxes, eight non‐allelic glossy mutants were subjected to transcriptomic comparisons with their respective wild‐type siblings. Transcriptomic comparisons identified 2279 differentially expressed (DE) genes. Other glossy genes tended to be down‐regulated in glossy mutants; by contrast stress‐responsive pathways were induced in mutants. Gene co‐expression network (GCN) analysis found that glossy genes were clustered, suggestive of co‐regulation. Genes that potentially regulate the accumulation of glossy gene transcripts were identified via a pathway level co‐expression analysis. Expression data from diverse organs showed that maize glossy genes are generally active in young leaves, silks, and tassels, while largely inactive in seeds and roots. Through reverse genetics, a DE gene homologous to Arabidopsis CER8 and co‐expressed with known glossy genes was confirmed to participate in epicuticular wax accumulation. GCN data‐informed forward genetics approach enabled cloning of the gl14 gene, which encodes a putative membrane‐associated protein. Our results deepen understanding of the transcriptional regulation of the genes involved in the accumulation of epicuticular wax, and provide two maize glossy genes and a number of candidate genes for further characterization. Significance Statement: Co‐expression, suggestive of co‐regulation, of the genes determining accumulation of waxes on the plant's outmost surface was found from gene expression analysis, which also identified transcription factors that are likely to participate in the transcriptional modulation of the wax pathway. With genes co‐expressed with known genes in the pathway, two unknown maize genes responsible for accumulation of surface waxes were experimentally confirmed, demonstrating a strategy to facilitate the identification of causal genes of certain traits. [ABSTRACT FROM AUTHOR]

Published
2019
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35. TheAux/IAAgenerum1involved in seminal and lateral root formation controls vascular patterning in maize (Zea maysL.) primary roots: Fig. 3.

Author

Zhang, Yanxiang, primary, Paschold, Anja, additional, Marcon, Caroline, additional, Liu, Sanzhen, additional, Tai, Huanhuan, additional, Nestler, Josefine, additional, Yeh, Cheng-Ting, additional, Opitz, Nina, additional, Lanz, Christa, additional, Schnable, Patrick S., additional, and Hochholdinger, Frank, additional

Published
2015
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37. B73-Mo17 Near-Isogenic Lines Demonstrate Dispersed Structural Variation in Maize

Author

Eichten, Steven, Foerster, Jillian M., de Leon, Natalia, Kai, Ying, Yeh, Cheng-Ting, Liu, Sanzhen, Jeddeloh, Jeffrey A., Schnable, Patrick S., Kaeppler, Shawn M., Springer, Nathan M, Eichten, Steven, Foerster, Jillian M., de Leon, Natalia, Kai, Ying, Yeh, Cheng-Ting, Liu, Sanzhen, Jeddeloh, Jeffrey A., Schnable, Patrick S., Kaeppler, Shawn M., and Springer, Nathan M

Abstract

Recombinant inbred lines developed from the maize (Zea mays ssp. mays) inbreds B73 and Mo17 have been widely used to discover quantitative trait loci controlling a wide variety of phenotypic traits and as a resource to produce high-resolution genetic maps. These two parents were used to produce a set of near-isogenic lines (NILs) with small regions of introgression into both backgrounds. A novel array-based genotyping platform was used to score genotypes of over 7,000 loci in 100 NILs with B73 as the recurrent parent and 50 NILs with Mo17 as the recurrent parent. This population contains introgressions that cover the majority of the maize genome. The set of NILs displayed an excess of residual heterozygosity relative to the amount expected based on their pedigrees, and this excess residual heterozygosity is enriched in the low-recombination regions near the centromeres. The genotyping platform provided the ability to survey copy number variants that exist in more copies in Mo17 than in B73. The majority of these Mo17-specific duplications are located in unlinked positions throughout the genome. The utility of this population for the discovery and validation of quantitative trait loci was assessed through analysis of plant height variation.

Published
2011

38. Parent-of-Origin Effects on Gene Expression and DNA Methylation in the Maize Endosperm

Author

Waters, Amanda J, Makarevitch, Irina, Eichten, Steven, Swanson-Wagner, Ruth, Yeh, Cheng-Ting, Xu, Wayne, Schnable, Patrick S., Vaughn, Matthew W, Gehring, Mary, Springer, Nathan M, Waters, Amanda J, Makarevitch, Irina, Eichten, Steven, Swanson-Wagner, Ruth, Yeh, Cheng-Ting, Xu, Wayne, Schnable, Patrick S., Vaughn, Matthew W, Gehring, Mary, and Springer, Nathan M

Abstract

Imprinting describes the differential expression of alleles based on their parent of origin. Deep sequencing of RNAs from maize (Zea mays) endosperm and embryo tissue 14 d after pollination was used to identify imprinted genes among a set of ~12, 000 genes that were expressed and contained sequence polymorphisms between the B73 and Mo17 genotypes. The analysis of parent-of-origin patterns of expression resulted in the identification of 100 putative imprinted genes in maize endosperm, including 54 maternally expressed genes (MEGs) and 46 paternally expressed genes (PEGs). Three of these genes have been previously identified as imprinted, while the remaining 97 genes represent novel imprinted maize genes. A genome-wide analysis of DNA methylation identified regions with reduced endosperm DNA methylation in, or near, 19 of the 100 imprinted genes. The reduced levels of DNA methylation in endosperm are caused by hypomethylation of the maternal allele for both MEGs and PEGs in all cases tested. Many of the imprinted genes with reduced DNA methylation levels also show endosperm-specific expression patterns. The imprinted maize genes were compared with imprinted genes identified in genome-wide screens of rice (Oryza sativa) and Arabidopsis thaliana, and at least 10 examples of conserved imprinting between maize and each of the other species were identified.

Published
2011

39. Heritable epigenetic variation among maize inbreds

Author

Eichten, Steve R., Swanson-Wagner, Ruth A., Schnable, James C., Waters, Amanda J., Hermanson, Peter J., Liu, Sanzhen, Yeh, Cheng-Ting, Jia, Yi, Gendler, Karla, Freeling, Michael, Schnable, Patrick S., Vaughn, Matthew W., Springer, Nathan M., Eichten, Steve R., Swanson-Wagner, Ruth A., Schnable, James C., Waters, Amanda J., Hermanson, Peter J., Liu, Sanzhen, Yeh, Cheng-Ting, Jia, Yi, Gendler, Karla, Freeling, Michael, Schnable, Patrick S., Vaughn, Matthew W., and Springer, Nathan M.

Abstract

Epigenetic variation describes heritable differences that are not attributable to changes in DNA sequence. There is the potential for pure epigenetic variation that occurs in the absence of any genetic change or for more complex situations that involve both genetic and epigenetic differences. Methylation of cytosine residues provides one mechanism for the inheritance of epigenetic information. A genome-wide profiling of DNA methylation in two different genotypes of Zea mays (ssp. mays), an organism with a complex genome of interspersed genes and repetitive elements, allowed the identification and characterization of examples of natural epigenetic variation. The distribution of DNA methylation was profiled using immunoprecipitation of methylated DNA followed by hybridization to a high-density tiling microarray. The comparison of the DNA methylation levels in the two genotypes, B73 and Mo17, allowed for the identification of approximately 700 differentially methylated regions (DMRs). Several of these DMRs occur in genomic regions that are apparently identical by descent in B73 and Mo17 suggesting that they may be examples of pure epigenetic variation. The methylation levels of the DMRs were further studied in a panel of near-isogenic lines to evaluate the stable inheritance of the methylation levels and to assess the contribution of cis- and trans- acting information to natural epigenetic variation. The majority of DMRs that occur in genomic regions without genetic variation are controlled by cis-acting differences and exhibit relatively stable inheritance. This study provides evidence for naturally occurring epigenetic variation in maize, including examples of pure epigenetic variation that is not conditioned by genetic differences. The epigenetic differences are variable within maize populations and exhibit relatively stable trans-generational inheritance. The detected examples of epigenetic variation, including some without tightly linked genetic variation, may con

Published
2011

40. Spreading of Heterochromatin Is Limited to Specific Families of Maize Retrotransposons

Author

Eichten, Steven R., primary, Ellis, Nathanael A., additional, Makarevitch, Irina, additional, Yeh, Cheng-Ting, additional, Gent, Jonathan I., additional, Guo, Lin, additional, McGinnis, Karen M., additional, Zhang, Xiaoyu, additional, Schnable, Patrick S., additional, Vaughn, Matthew W., additional, Dawe, R. Kelly, additional, and Springer, Nathan M., additional

Published
2012
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42. Genic and nongenic contributions to natural variation of quantitative traits in maize

Author

Li, Xianran, primary, Zhu, Chengsong, additional, Yeh, Cheng-Ting, additional, Wu, Wei, additional, Takacs, Elizabeth M., additional, Petsch, Katherine A., additional, Tian, Feng, additional, Bai, Guihua, additional, Buckler, Edward S., additional, Muehlbauer, Gary J., additional, Timmermans, Marja C.P., additional, Scanlon, Michael J., additional, Schnable, Patrick S., additional, and Yu, Jianming, additional

Published
2012
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43. Parallel domestication of the Shattering1 genes in cereals

Author

Lin, Zhongwei, primary, Li, Xianran, additional, Shannon, Laura M, additional, Yeh, Cheng-Ting, additional, Wang, Ming L, additional, Bai, Guihua, additional, Peng, Zhao, additional, Li, Jiarui, additional, Trick, Harold N, additional, Clemente, Thomas E, additional, Doebley, John, additional, Schnable, Patrick S, additional, Tuinstra, Mitchell R, additional, Tesso, Tesfaye T, additional, White, Frank, additional, and Yu, Jianming, additional

Published
2012
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45. Heritable Epigenetic Variation among Maize Inbreds

Author

Eichten, Steve R., primary, Swanson-Wagner, Ruth A., additional, Schnable, James C., additional, Waters, Amanda J., additional, Hermanson, Peter J., additional, Liu, Sanzhen, additional, Yeh, Cheng-Ting, additional, Jia, Yi, additional, Gendler, Karla, additional, Freeling, Michael, additional, Schnable, Patrick S., additional, Vaughn, Matthew W., additional, and Springer, Nathan M., additional

Published
2011
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48. Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content

Author

Springer, Nathan M., primary, Ying, Kai, additional, Fu, Yan, additional, Ji, Tieming, additional, Yeh, Cheng-Ting, additional, Jia, Yi, additional, Wu, Wei, additional, Richmond, Todd, additional, Kitzman, Jacob, additional, Rosenbaum, Heidi, additional, Iniguez, A. Leonardo, additional, Barbazuk, W. Brad, additional, Jeddeloh, Jeffrey A., additional, Nettleton, Dan, additional, and Schnable, Patrick S., additional

Published
2009
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50. Image Integrity Verification Using Content-Based Watermarking

Author

Yeh, Cheng-Ting Eddy

Abstract

Digital watermarking is a technique to insert an information-carrying digital signature into a digital media so that the signature can be extracted for variety of purposes including ownership authentication and content verification. In recent years, the popularity of the Internet and increase of sophisticated image processing tools commercially available today have created opportunities for malicious parties to intercept images, modify its content, and then transmit the forgeries to their respective receivers, where alterations resemble closely to the work of professionals and are undetectable by the human eye. For this reason, in order to reduce the constant proliferation and threats for digital media in the World Wide Web, digital watermarking is one of the crucial techniques to protect the contents of products in digital form and enable copyright or ownership information to be embedded into the multimedia data. The purpose of this study was to examine the weaknesses against common watermarking attacks of blockwise independent and content-based watermarking algorithms for image integrity verification and implement a new and more secure invisible fragile watermarking technique for color or grayscale images that increases the message digest size from the proposed 64 to 128 bits using the same small-size blocks and maintaining accurate localization of image changes. Our watermarking technique is capable to detect any changes made to the image since the time it was stamped, any changes to the pixel values and also to the dimensions of the image will be automatically detected and localized. Our scheme consists of a watermark insertion process that uses a private key to embed a watermark image into a cover image, and a watermark extraction process that uses a public key to extract the watermark from the watermarked image. The embedded watermark can only be extracted by someone who has possession of a proper verification key. This implies that someone who does not have a valid key will not be able to forge a watermark that will pass undetected. Finally, our technique provides means of ensuring data integrity; adds more security to the contents of digital media and allows recipients of an image to verify its authenticity with ease as well as display the ownership information embedded within an image.

Published
2005

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